rs7241142

Variant names:

• chr18-894241-G-A
• rs7241142
• ENST00000582554.1:n.*194C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-894241-G-A
• chr18-894241-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000582554.1(ENSG00000265671):​n.*194C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,976 control chromosomes in the GnomAD database, including 31,076 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (31076 hom., cov: 31)
• Consequence: ENSG00000265671 ENST00000582554.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

ENSG00000265671 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265671	ENST00000582554.1	n.*194C>T		downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93894 AN: 151858 Hom.: 31073 Cov.: 31

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.646

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.618 AC: 93925 AN: 151976 Hom.: 31076 Cov.: 31 AF XY: 0.621 AC XY: 46152 AN XY: 74276

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.649

Alfa AF: 0.663 Hom.: 5874

Bravo AF: 0.610

Asia WGS AF: 0.734 AC: 2552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7241142; hg19: chr18-894242;